[BioC] Error Message with RMA normalization in AgiMicroRNA

[James W. MacDonald]

Hi Richard,

Richard Friedman wrote:
> Dear Bioconductor List,
> 
> 	I received an error message when trying to normalize data with  
> AgiMicroRMA
>  > agiMicro.rma=rmaMicroRna(agiMicroraw,
> + 		normalize=TRUE,
> +  		background=FALSE)
> Error in if (min(dd.aux$Rb) < 0) { :
>    missing value where TRUE/FALSE needed
>  > agiMicro.rma=rmaMicroRna(agiMicroraw,
> + 		normalize=TRUE,
> +  		background=TRUE)
> Error in if (min(dd.aux$Rb) < 0) { :
>    missing value where TRUE/FALSE needed

It looks like you have some NA values in agiMicroraw$Rb, so I would 
check that first. I don't see any code in rmaMicroRna() to gracefully 
handle missing data, so that is likely the problem.

If there aren't any NA values in agiMicroraw$Rb, then you should try 
debuggind rmaMicroRna() to see where things are going wrong. Simply 
start with

debug(rmaMicroRna)

and then

agiMicro.rma <- rmaMicroRna(agiMicroraw, TRUE, FALSE)

you will then go into the browser, and can step through the function 
until you get to

ProbeName.rep = unique(dd$genes$ProbeName[duplicated(dd$genes$ProbeName)])
dd.aux = dd[1:length(ProbeName.rep), ]

at which time you can look for NA values in dd.aux$Rb, and try to track 
down where they come from. But looking at the code, I don't see any 
obvious way for them to be produced if not already there.

Best,

Jim


>  >
> ################################################################################
> My session Inforrmation is:
> 
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-apple-darwin9.8.0
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] AgiMicroRna_1.2.0     preprocessCore_1.10.0 affy_1.26.1            
> limma_3.4.0
> [5] Biobase_2.8.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0
>  >
> ################################################################################
> 
> 
> My session up to the attempt to normalize is:
> #################################################################################
> 
> 
>  > targets<-readTargets("Targets.txt",verbose=TRUE)
> 
> Target File
>                         FileName Treatment GErep
> AxCNTx1x1x1     AxCNTx1x1x1.txt     A.CNT     1
> AxCNTx2x2x2     AxCNTx2x2x2.txt     A.CNT     1
> AxCNTx3x3x3     AxCNTx3x3x3.txt     A.CNT     1
> AxCNTx7x4x4     AxCNTx7x4x4.txt     A.CNT     1
> BxCCL4x1x1x5   BxCCL4x1x1x5.txt    B.CCL4     2
> BxCCL4x2x2x6   BxCCL4x2x2x6.txt    B.CCL4     2
> BxCCL4x3x3x7   BxCCL4x3x3x7.txt    B.CCL4     2
> BxCCL4x5x4x8   BxCCL4x5x4x8.txt    B.CCL4     2
> CxBDLx1x1x9     CxBDLx1x1x9.txt     C.BDL     3
> CxBDLx2x2x10   CxBDLx2x2x10.txt     C.BDL     3
> CxBDLx3x3x11   CxBDLx3x3x11.txt     C.BDL     3
> CxBDLx4x4x12   CxBDLx4x4x12.txt     C.BDL     3
> DxaHSCx1x1x13 DxaHSCx1x1x13.txt    D.aHSC     4
> DxaHSCx2x2x14 DxaHSCx2x2x14.txt    D.aHSC     4
> DxaHSCx3x3x15 DxaHSCx3x3x15.txt    D.aHSC     4
> DxaHSCx4x4x16 DxaHSCx4x4x16.txt    D.aHSC     4
> 
>  > agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE)
> Read AxCNTx1x1x1.txt
> Read AxCNTx2x2x2.txt
> Read AxCNTx3x3x3.txt
> Read AxCNTx7x4x4.txt
> Read BxCCL4x1x1x5.txt
> Read BxCCL4x2x2x6.txt
> Read BxCCL4x3x3x7.txt
> Read BxCCL4x5x4x8.txt
> Read CxBDLx1x1x9.txt
> Read CxBDLx2x2x10.txt
> Read CxBDLx3x3x11.txt
> Read CxBDLx4x4x12.txt
> Read DxaHSCx1x1x13.txt
> Read DxaHSCx2x2x14.txt
> Read DxaHSCx3x3x15.txt
> Read DxaHSCx4x4x16.txt
> 
>    RGList:
> 	dd$R:		'gTotalGeneSignal'
> 	dd$G:		'gTotalProbeSignal'
> 	dd$Rb:		'gMeanSignal'
> 	dd$Gb:		'gProcessedSignal'
> 
> 
> 
>  > agiMicro.rma=rmaMicroRna(agiMicroraw,
> + 		normalize=TRUE,
> +  		background=FALSE)
> Error in if (min(dd.aux$Rb) < 0) { :
>    missing value where TRUE/FALSE needed
> ################################################################################
> 
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
> 
> In Memoriam,
> George Scithers
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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